Subsurface heterogeneity is found across the whole hydrological cycle. It causes preferential flow in the soil, the vadose zone, and the bedrock. Aside of this, it has many other consequences for water flow and storage. This opinion paper discusses the implications of subsurface heterogeneity across the hydrological cycle and its implications for hydrological modeling. It focuses on the representation (and misrepresentation) of subsurface heterogeneity within hydrological models at different scales. Possible limitations to the prediction performance of hydrological models that disregard subsurface heterogeneity are introduced and discussed. The paper ends with practical recommendations to include subsurface heterogeneity into hydrological models, to parameterize them realistically, and to present possible directions for future research.